Datasets:

markfaa
/

CryoAtlas

CryoAtlas v1.0 pairs experimental cryo-EM density maps with atomic structures and protein sequences, using EMDB and PDB records available up to March 2026. Entries undergo map–model alignment, sequence mapping, and quality filtering to support research on automated protein atomic model building.

The complete release is available here: four training parts, the full test set, and benchmark resources. The 70 training and test archives total 2.415 TB (decimal units); their sizes and SHA-256 hashes have been verified against the frozen v1.0 release.

Browse before downloading

The Dataset Viewer above displays lightweight tables and image previews. Select a configuration from its dropdown:

Configuration	Contents	Useful for
`catalog` — default	16,657 training and 1,152 test rows	Search EMD/PDB IDs, resolution and titles; find the archive containing an entry
`benchmark_targets`	The 618 common benchmark targets	Inspect the exact evaluation subset
`benchmark_results`	3,090 rows: 618 targets × five methods	Compare released metrics using the `emd_id` and `method` columns
`training_utility`	1,236 rows: 618 targets × two retraining conditions	Compare released ModelAngelo CNN retraining results
`examples`	Density projections for 10 example entries	Inspect sample maps without downloading a large archive
`downloads`	71 archives, including benchmark resources	Check sizes, entry counts, download URLs and SHA-256 hashes

The original per-method CSVs remain available in benchmark/results/. Use the method column in the unified results table to select a method.

The catalog contains metadata and archive links; map, CIF and FASTA payloads reside in the archives. Field definitions and provenance explain the tables and previews.

Download the data you need

Component	Entries	Archives	Compressed size	Files
Training Part 1	4,164	17	560.0 GB	Browse
Training Part 2	4,164	17	563.0 GB	Browse
Training Part 3	4,165	17	564.9 GB	Browse
Training Part 4	4,164	17	575.8 GB	Browse
Benchmark test subset	618	1	81.9 GB	Download
Remaining test entries	534	1	69.0 GB	Download
Benchmark resources	Results, predictions and 10 examples	1	1.90 GB	Download

The four training parts are disjoint download partitions of one fixed split. 618 + 534 = 1,152 test entries: the benchmark is a subset of the test set, not an additional split. The 618 targets support paired comparisons after training-overlap filtering and selection of targets with valid outputs from the evaluated learning-based methods. The remaining entries complete the fixed test split.

For a first look, use the online previews or the 1.90 GB benchmark resource archive. To locate a particular entry or download a selected training part, use the download helper:

pip install -U huggingface_hub
hf download markfaa/CryoAtlas resources/scripts/download.py --repo-type dataset --local-dir .

# Show the archive and size for one entry; do not download the archive yet.
python resources/scripts/download.py --emd EMD-0719 --dry-run

# Download Training Part 1 and verify each archive.
python resources/scripts/download.py --part 1 --destination CryoAtlas-downloads

--emd selects the complete archive containing that entry. More options, direct downloads, extraction instructions and checksum commands are in the download guide.

Repository layout

README.md                 Short introduction and main download links
train/part01/ ... part04/  68 training archives
test/                     Two test archives
resources/                Benchmark resource package and supporting files
    benchmark/            Evaluation tables and image previews
    metadata/             Source accessions, splits, inventories, catalogs and checksums
    docs/                 Detailed documentation and figures
    scripts/              Selective download helper

Repository-side supporting paths are grouped under resources/. Paths inside extracted archives retain their original v1.0 layout.

What is inside an entry?

Training and test archives extract into CryoAtlas_v1.0/train/EMD-.../ and CryoAtlas_v1.0/test/EMD-.../. Each archive is independently extractable; extract the desired archives into the same parent directory.

File	Contents
`emd_<id>_fullmap.map`	Experimental density map in MRC/CCP4 format
`<pdb>.cif`	Atomic structure with deposited metadata
`<pdb>.fasta`	Original protein sequence records
`<pdb>_aligned.fasta`	Aligned sequences, including gap characters where applicable
`<pdb>_trimmed.fasta`	Terminal-trimmed sequences
`<pdb>_aligned.cif`, where supplied	Structure aligned to the density-map frame

Use the aligned CIF for map-frame comparisons when it is provided. The per-archive inventories record the exact files and hashes for each entry.

Benchmark resources and examples

Visit the CryoAtlas project website for the paper overview and the 3D Benchmark Explorer for interactive structure and density visualization.

The resource archive extracts into CryoAtlas_v1.0_resources/. It contains:

Benchmark_outcome/: the five original evaluation CSVs, with 618 target rows each.
Benchmark_rawdata/: predicted CIF files from AF3, CryoAtom2, E3-CryoFold, EMProt and ModelAngelo, with 618 targets per method.
metadata/: source accessions, fixed split lists, alignment availability and resource-file checksums.
training_utility/: MA_CryoAtlas.csv and MA_Cryo2StructData.csv (618 target rows plus one AVERAGE row each), with the corresponding MA_CryoAtlas/ and MA_Cryo2StructData/ predicted CIF folders (618 per condition). These are existing paper results from the original Kaggle resource release.
sample/Dataset/: 10 self-contained examples with maps, structures, sequences and available predictions.

The same five CSVs are available directly in this repository under resources/benchmark/results/. The unified Viewer table adds a method column and removes method prefixes from column names; it preserves the released measurements. AF3 is a sequence-based reference; the other four methods use density maps.

Example gallery

Nine examples belong to the 618-target benchmark. EMD-0719 belongs to training, includes an aligned CIF, and has no baseline predictions in the example package. These examples also occur in the full release and do not add new entries.

Open the image Viewer

Show all 10 density previews

Previews show maximum-intensity projections along the three stored array axes. Each view uses its own 2nd–99.5th percentile display range. They are visual summaries, not aligned structure overlays or quantitative map-quality measurements. Original maps are available in the resource archive and full release.

Provenance, scope and license

Source accessions identify EMDB/PDB records and original map URLs. Fixed split lists, per-part EMD lists, file inventories and checksums support reproducible retrieval. The overview and catalog use the published metadata; no scientific data or benchmark measurements were modified during repository organization.

CryoAtlas supports protein atomic model building from cryo-EM maps. The benchmark results describe the released methods and evaluation subset; the 10 examples are for inspection, not an independent evaluation set.

The dataset and benchmark resources are distributed under CC BY-NC 4.0. Source attribution and deposited metadata are retained.